Students will gain familiarity with fundamental concepts in molecular biology, probabilistic approaches for sequence alignment and protein structure inference, as well as the application of physical models to understand cellular functions.

Basics of probability theory, principles of statistical physics, basic programming skills.

• Elements of molecular biology: DNA, RNA, proteins. • Inference techniques: sequence alignments, structural inference, phylogeny reconstruction. • Physical biology of the cell: gene regulation, cell compartments, vesicle trafficking, metabolism.

The course alternates lectures on theoretical topics (approximately 48 hours) and hands-on computer lab (approximately 12 hours). During the computer labs, students will have the opportunity to apply theoretical concepts and algorithms to specific problem scenarios.

• Course handouts • R. Phillips et al, Physical Biology of the Cell, Garland Science, 2012 • P. Nelson, Biological physics, Freeman, 2004 • M. Kardar and L. Mirny, Statistical Physics in biology, MIT OpenCourseWare 8.592J / HST.452J • B. Alberts et al., Molecular Biology of the Cell, Garland Science, 2015 • R. Durbin et al., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge Un. Press, 2002 • H.C. Nguyen, R. Zecchina and J. Berg, Inverse statistical problems: from the inverse Ising problem to data science, Adv. Phys., 66 (2017) 197-261. • S. Cocco et al., Inverse statistical physics of protein sequences: a key issues review, Rep. Progr. Phys. 81 (2018) 032601. • J. Felsenstein, Inferring phylogenies, Sinauer Associates, 2004 • Suggested scientific publications

Text book;

You can take this exam before attending the course

Exam: Compulsory oral exam;

To gain access to the oral exam, students will be required to individually complete and submit the results of the computing assignments assigned during the laboratory sessions. The oral exam entails a comprehensive presentation of a scientific work chosen by the student from the ones discussed in the course and uploaded in the 'Material' section of the course site. Alternatively, students may select other works related to the course topics, subject to approval by the instructors. The presentation will be followed by 2-3 broad questions covering the main topics covered in the lectures. The grading of the presentation contributes to one-third of the overall assessment, with a maximum grade of 30L. The purpose of the exam is to assess the student's comprehension of fundamental concepts in molecular biology, probabilistic approaches to sequence alignment, inference of protein structures, and physical modeling of cellular functions.

In addition to the message sent by the online system, students with disabilities or Specific Learning Disorders (SLD) are invited to directly inform the professor in charge of the course about the special arrangements for the exam that have been agreed with the Special Needs Unit. The professor has to be informed at least one week before the beginning of the examination session in order to provide students with the most suitable arrangements for each specific type of exam.